Not by personal preference mate, it's my profession, don't put 6x9s in the rear shelf, especially if you intend on putting subs in the boot, I've put infinity 6.5s in the reAr of kez's and it sounds loads better,
Honestly mate, decent sub and 6.5s powered by an amp will sound much better than any 6x9 and sub set up
Think about it, what is a sub designed to do, move large amounts of air which creates bass, and the boot in a car helps as it creates another 'box' for sub, listen to a sub in a car the. Remove the seats, loads different,
With the 6x9s in the shelf, all the pressure push's on the cones of the 6x9s, making them sound shit,
Also, sound is essentially 3 things
High notes
Low notes
And mids
Tweeters create high notes, subs low notes, 6x9s make low notes and high, although if you have a sub you already have bass, which again makes them pointless, and the music will sound crap, 6.5s provide a great amount of mid, and make the music sound 'fuller'
Yeah 6x9s may make your cAr sound bassier and make stuff rattle, but they sound shit and aren't needed